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Jawaharlal Nehru Krishi
VishwaVidyalaya, Jabalpur
(2016-17)
Credit seminar on
Guided by-
Dr. D.K. MISHRA
Submitted by-
Srishti Singh
Roll no 6527
M.Sc. (Ag) final year
FORWARD
GENETICS
REVERSE
GENETICS
A
N
D
TOPICW
E
L
C
O
M
E
GENETICS
•Science that deals with the structure,organisation,transmission
and function of genes, and the origin of variation
•Founder -Mendal in 1866
•Terms given by-Bateson in 1905
By:Wikipedia
Background
•Genetics is the study of gene function
•Gene function is inferred from the resulting phenotype when the
gene is mutated
•Genomics is changing the way of genetics is performed Globally,i.e.
high-throughput approaches
•Genomics approaches are being applied to both forward and reverse
genetics
GENETICS
FORWARD GENETICS REVERSE GENETICS
Forward
Genetics
Forward genetics starts with identification of interesting mutant
phenotype
AIM
Then aims to discover the function of genes defective in
mutants by chromosome walking
chromosome contig candidate genes mutation
To find all of the genes involved in a trait
•Forward genetics usually starts with mutagenesis of organism Can use
chemicals
e.g., ethyl methyl sulfonate
Or can use radiation
e.g., X rays, gamma rays
•Then screen progeny of mutagenized individuals for phenotypes of
interest
BASICS OF FORWARD GENETICS
Visually- abnormal morphology, growth rate, color, flowering, fertility,
etc.
Biochemically— alterations in basic cell
processes (replication, protein synthesis, etc.)
Microscopically (use fluorescent tags
to see overexpression) and image analysis
How do scientists screen phenotypes?
http://www.illuminatedcell.com/autophagosomes.html
Genetic analysis
First step in analysis of mutants:
• Precisely describe phenotype
Basis of predicting gene function:
•identify precisely what has malfunctioned (wrong) in the
mutant
•That is what the gene product does in the wild type
STEPS IN FORWARD GENETICS
A set of mutants lines are created either by EMS and/or TDNA /
transposon preferably called as knockout for the latter.
These mutant lines are then screened for a particular phenotype usin
g mutant screens or procedures where a large number of
mutants can be screened in a bulk manner
The selected mutants are then carried forward and analyzed by PCR (i
n case of TDNA insertion lines), backcrossed to remove
or dilute any unwanted insertions of TDNA
The next logical steps involves cloning of the full length gene an
d cDNA from the wild type plants.
In the final validation step, the gene isolated in the previous step is use
d to transform the mutant plant and phenotyped.
“If
Themutant plant exhibits recovery of wild type phenotype, it is assume
d that the wt type gene is able to rescue the mutant; hence
this validates the gene function.”
The sequence information generated from the PCR is then used to ident
ify the gene where the insertion has taken place and this
becomes the candidate gene for the phenotype tested in previous
steps.
Genomics and forward genetics
High-throughput genetic screens
•Candidate-gene approach
To go from phenotype to gene
•Insertional mutagenesis
Loss-of-function mutation Activation tagging
•Enhancer trapping
High-throughput genetic screen
Paradigm Genetics, Inc.
performs “phenotypic
profiling”
Take measurements of
mutants’ physical and
chemical parameters
e.g., plant height, leaf size,
root density, and nutrient
utilization
Different developmental
times: compare to wild type
From phenotype to gene
Once an interesting
mutant is found and
characterized, we
want to find the gene
in which the mutant
occurred
Positional cloning
•First use genetic
mapping
•Then use
chromosome
walking
chromosome contig
candidate genes mutation
Candidate-gene approach
If the mutated gene is localized to a sequenced region
of the chromosome, then look for genes that could be
involved in the process under study
Last step:
•confirm gene identification
•Rescue of phenotype
•Mutations in same gene in different alleles
Insertional mutagenesis
•Alternative to chromosome walking
•To reduce time and effort required to identify mutant gene
•Insert piece of DNA that disrupts genes
•Inserts randomly in chromosomes
•Make collection of individuals
•Each with insertion in different place
•Screen collection for phenotypes
•Use inserted DNA to identify mutated gene :Researchgate
Insertional mutagenesis in Arabidopsis
• T-DNA inserts into plant
chromosome
• Screen for mutations
that affect flower
formation
• Make genomic library
from mutant DNA
• Probe with T-DNA
• Identify mutant gene
T-DNA
inserts
into
gene
probe library
made from
T-DNA tagged
mutant with
T-DNA
sequence
DNA flanking
T-DNA to
identify gene
Enhancer trapping
• Type of insertional mutagenesis
– Used to find genes with interesting expression
patterns
• Insert carries a reporter gene
– Expresses foreign protein
– No effect on organism
• Enhancer trap
– Has minimal promoter in front of reporter gene
– Enhancer near point of insertion acts on it
Enhancer trapping in Drosophila
• Use transposon P
element
• Carries reporter gene
– b-galactosidase
• Hops into genome
• When lands near
enhancer, activates gene
expression
• Expression similar to that
of neighboring gene
P element recognition sites
enhancer gene Y
enhancer b-galactosidase
b-galactosidase
gene Y
Advantages and disadvantages of Forward genetics
 It is a tested method and many genes have been isolated in plants.
 It works very well in phenotypes that can be distinguished
quickly, for eg. color, shape etc.
 It works in a unbiased manner because it is random in natureThe
mutant lines created are quite stable and T-
DNA is known to preferentially integrate in and around the genic
region
 On the other hand, phenotypes that are difficult to evaluate mak
e it very tedious.
 Only one gene/trait can be analyzed
 Some genes may be missed and the procedure works only in plan
ts that are amenable to Agrobacterium transformation
REVERSE GENETICS
Reverse genetics starts with a known gene and alters
its function by transgenic technology
AIM
Then aims to determine the role of the gene from the
effects on the organism
AGCTCAATAGATAATC
TCGAGTTAGTCTATTAG
Sequence/mutation DNA Phenotype
Basics of reverse genetics
To find out the function of a known gene
• Reverse genetics starts with known genes
– e.g., from genomic sequencing
• to determine function through targeted
modulation of gene activity
Decrease
Increase
Reverse Genetics Techniques
Virus indused gene silencing
Chemical mutagenesis or TILLING
RNA mediated interfernce (RNAi)
DELETEAGENES
Virus indused gene silencing(VIGS) eg: zebra fish
Injection of zebra fish embryo with retrovirus preparation
Raising of founder embryo generation
F1 generation by inbreeding/outbreeding of founder
Identification of F1 fish with multiple insertions
Raising F2 families by inbreeding selected F1 fishes
Sperms were collected and archived from 2nd and 3rd
generation
DNA extracted from fin clips
Insertion sites were identified by LM-PCR and
sequencing
Eg. Arabidopsis
RNA mediated interfernce (RNAi)
•Suppresses gene expression
•Post-transcriptional biological process
•mRNA degradation/ inhibition of
translation
•Target - dsRNA
The Mechanism of RNA Interference
DELETEAGENES useful for small genes and tandem repeats
Deletion library construction
Treat wild type seeds with fast neutron
Plant M1 seeds and grow up population
Collect M2 seeds from individual plants
Plant some seeds from each line
Collect tissue and extract DNA
Fast Neutron Deletion Mutagenesis-based Reverse Genetics
Approach for Plants
TILLING is a general reverse genetic technique that
combines chemical mutagenesis with PCR based screening to
identify point mutations in regions of interest. (McCallum
et.al, 2000)
(Targeting Induced Local Lesions IN Genomes)
TILLING
TILLING first began in the late 1990’s by McCallum
who worked on characterizing the function of two
chromomethylase gene in Arabidopsis.
 Development of mutagenized population
EMS mutagenesis
Development of M2 population
 DNA preparation and pooling of individuals
 Mutation Discovery
PCR amplification of a region of interest
Mismatched cleavage
Detection of Heteroduplexes as extra peak or band (HPLC
or Acrylamide gel)
Identification of the mutant individual
Sequencing of Mutant PCR product
The TILLING Methodology
The TILLINGpopulation-MUTAGENESIS
Mutagenizing seed with EMS done by soaking seeds in an EMS
solution (14-18 h in a 30-100 mM (0.3%-1%) EMS solution.)
Planting the seeds in field
Mutagenized population (M1generation) is grown to maturity
allowed to self-fertilize to produce M2 seeds.
M2 seeds can be maintained as lines or bulked
If the M2 seed is bulked then lines need to be established using M3 seed.
In either case, when sampling M2 plants to establish population
Arraying the population for TILLING
Genomic DNA is isolated from individuals M2/M3 plants
Standardized the DNA concentration of each sample
Arrayed in a 96-well microtiter plate
Allowing up to 8-fold pooling of diploid plants to increase
TILLING throughput
Tilling in soybean
Advantages
Its applicability to virtually any organism.
Its facility for high-throughput and its independence of genome
size, reproductive system or generation time.
Since it uses Chemical mutagenesis virtually all genes can be
targeted by screening few individuals.
High degree of mutational saturation can be achieve without
excessive collateral DNA damage.
Eco- TILLING is useful for association mapping study and linkage
disequilibrium analysis.
Ecotilling can be used not only to determine the extent of variation
but also to assay the level of heterozygosity within a gene.
EcoTILLING
The first publication of the EcoTILLING method in which
TILLING was modified to mine for natural polymorphisms
was in 2004 from work in Arabidopsis thaliana.
EcoTILLING is similar to TILLING, except that its objective
is to identify natural genetic variation as opposed to induced
mutations.
Many species are not amenable to chemical mutagenesis;
therefore, EcoTILLING can aid in the discovery of
natural variants and their putative gene function
This approach allows one to rapidly screen through many
samples with a gene of interest to identify naturally occurring
SNPs and / or small INs/DELS.
TILLING and EcoTILLING
CASE STUDY- TILLING
CASE STUDY
Forward genetics in a reverse way
REFERENCES
Azpiroz-Leehan, R., and Feldmann, K.A. (1997).T-DNA insertion
mutagenesis in Arabidopsis: Going back and forth. Trends Genet. 13,
152–159.
Bradelly J Till et al.,(.2004) Discovery of induced mutation in maize by
TILLING:BMC Plant biology.4,471-2229
Krysan, P.J., Young, J.C., and Sussman, M.R. (1999). T-DNA as an
insertional mutagen in Arabidopsis. Plant Cell 11, 2283–2290
Parinov, S., and Sundaresan, V. (2000). Functional genomics in
Arabidopsis: Large-scale insertional mutagenesis complements the
genome sequencing project. Curr. Opin. Biotechnol. 11, 157–161.
Sussman, M.R., Amasino, R.M., Young, J.C., Krysan, P.J., and Austin-
Phillips, S. (2000). The Arabidopsis knockout facility at the University of
Wisconsin-Madison. Plant Physiol. 124, 1465–1467.
Also seen
• www.apsnet.org/edcenter/advan
ced/topics/Pages/ReverseGeneticT
ools.aspx
•http://www.illuminatedcell.com/a
utophagosomes.html
•https://www.ncbi.nlm.nih.gov ›
NCBI › Literature › PubMed Central
(PMC)
Forward and reverse genetics

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Forward and reverse genetics

  • 1. Jawaharlal Nehru Krishi VishwaVidyalaya, Jabalpur (2016-17) Credit seminar on Guided by- Dr. D.K. MISHRA Submitted by- Srishti Singh Roll no 6527 M.Sc. (Ag) final year
  • 3. GENETICS •Science that deals with the structure,organisation,transmission and function of genes, and the origin of variation •Founder -Mendal in 1866 •Terms given by-Bateson in 1905 By:Wikipedia
  • 4. Background •Genetics is the study of gene function •Gene function is inferred from the resulting phenotype when the gene is mutated •Genomics is changing the way of genetics is performed Globally,i.e. high-throughput approaches •Genomics approaches are being applied to both forward and reverse genetics GENETICS FORWARD GENETICS REVERSE GENETICS
  • 5. Forward Genetics Forward genetics starts with identification of interesting mutant phenotype
  • 6. AIM Then aims to discover the function of genes defective in mutants by chromosome walking chromosome contig candidate genes mutation To find all of the genes involved in a trait
  • 7. •Forward genetics usually starts with mutagenesis of organism Can use chemicals e.g., ethyl methyl sulfonate Or can use radiation e.g., X rays, gamma rays •Then screen progeny of mutagenized individuals for phenotypes of interest BASICS OF FORWARD GENETICS
  • 8. Visually- abnormal morphology, growth rate, color, flowering, fertility, etc. Biochemically— alterations in basic cell processes (replication, protein synthesis, etc.) Microscopically (use fluorescent tags to see overexpression) and image analysis How do scientists screen phenotypes? http://www.illuminatedcell.com/autophagosomes.html
  • 9. Genetic analysis First step in analysis of mutants: • Precisely describe phenotype Basis of predicting gene function: •identify precisely what has malfunctioned (wrong) in the mutant •That is what the gene product does in the wild type
  • 10. STEPS IN FORWARD GENETICS A set of mutants lines are created either by EMS and/or TDNA / transposon preferably called as knockout for the latter. These mutant lines are then screened for a particular phenotype usin g mutant screens or procedures where a large number of mutants can be screened in a bulk manner The selected mutants are then carried forward and analyzed by PCR (i n case of TDNA insertion lines), backcrossed to remove or dilute any unwanted insertions of TDNA
  • 11. The next logical steps involves cloning of the full length gene an d cDNA from the wild type plants. In the final validation step, the gene isolated in the previous step is use d to transform the mutant plant and phenotyped. “If Themutant plant exhibits recovery of wild type phenotype, it is assume d that the wt type gene is able to rescue the mutant; hence this validates the gene function.” The sequence information generated from the PCR is then used to ident ify the gene where the insertion has taken place and this becomes the candidate gene for the phenotype tested in previous steps.
  • 12. Genomics and forward genetics High-throughput genetic screens •Candidate-gene approach To go from phenotype to gene •Insertional mutagenesis Loss-of-function mutation Activation tagging •Enhancer trapping
  • 13. High-throughput genetic screen Paradigm Genetics, Inc. performs “phenotypic profiling” Take measurements of mutants’ physical and chemical parameters e.g., plant height, leaf size, root density, and nutrient utilization Different developmental times: compare to wild type
  • 14. From phenotype to gene Once an interesting mutant is found and characterized, we want to find the gene in which the mutant occurred Positional cloning •First use genetic mapping •Then use chromosome walking chromosome contig candidate genes mutation
  • 15. Candidate-gene approach If the mutated gene is localized to a sequenced region of the chromosome, then look for genes that could be involved in the process under study Last step: •confirm gene identification •Rescue of phenotype •Mutations in same gene in different alleles
  • 16. Insertional mutagenesis •Alternative to chromosome walking •To reduce time and effort required to identify mutant gene •Insert piece of DNA that disrupts genes •Inserts randomly in chromosomes •Make collection of individuals •Each with insertion in different place •Screen collection for phenotypes •Use inserted DNA to identify mutated gene :Researchgate
  • 17. Insertional mutagenesis in Arabidopsis • T-DNA inserts into plant chromosome • Screen for mutations that affect flower formation • Make genomic library from mutant DNA • Probe with T-DNA • Identify mutant gene T-DNA inserts into gene probe library made from T-DNA tagged mutant with T-DNA sequence DNA flanking T-DNA to identify gene
  • 18. Enhancer trapping • Type of insertional mutagenesis – Used to find genes with interesting expression patterns • Insert carries a reporter gene – Expresses foreign protein – No effect on organism • Enhancer trap – Has minimal promoter in front of reporter gene – Enhancer near point of insertion acts on it
  • 19. Enhancer trapping in Drosophila • Use transposon P element • Carries reporter gene – b-galactosidase • Hops into genome • When lands near enhancer, activates gene expression • Expression similar to that of neighboring gene P element recognition sites enhancer gene Y enhancer b-galactosidase b-galactosidase gene Y
  • 20. Advantages and disadvantages of Forward genetics  It is a tested method and many genes have been isolated in plants.  It works very well in phenotypes that can be distinguished quickly, for eg. color, shape etc.  It works in a unbiased manner because it is random in natureThe mutant lines created are quite stable and T- DNA is known to preferentially integrate in and around the genic region  On the other hand, phenotypes that are difficult to evaluate mak e it very tedious.  Only one gene/trait can be analyzed  Some genes may be missed and the procedure works only in plan ts that are amenable to Agrobacterium transformation
  • 21. REVERSE GENETICS Reverse genetics starts with a known gene and alters its function by transgenic technology
  • 22. AIM Then aims to determine the role of the gene from the effects on the organism AGCTCAATAGATAATC TCGAGTTAGTCTATTAG Sequence/mutation DNA Phenotype
  • 23. Basics of reverse genetics To find out the function of a known gene • Reverse genetics starts with known genes – e.g., from genomic sequencing • to determine function through targeted modulation of gene activity Decrease Increase
  • 24. Reverse Genetics Techniques Virus indused gene silencing Chemical mutagenesis or TILLING RNA mediated interfernce (RNAi) DELETEAGENES
  • 25. Virus indused gene silencing(VIGS) eg: zebra fish Injection of zebra fish embryo with retrovirus preparation Raising of founder embryo generation F1 generation by inbreeding/outbreeding of founder Identification of F1 fish with multiple insertions
  • 26. Raising F2 families by inbreeding selected F1 fishes Sperms were collected and archived from 2nd and 3rd generation DNA extracted from fin clips Insertion sites were identified by LM-PCR and sequencing Eg. Arabidopsis
  • 27.
  • 28. RNA mediated interfernce (RNAi) •Suppresses gene expression •Post-transcriptional biological process •mRNA degradation/ inhibition of translation •Target - dsRNA
  • 29. The Mechanism of RNA Interference
  • 30. DELETEAGENES useful for small genes and tandem repeats Deletion library construction Treat wild type seeds with fast neutron Plant M1 seeds and grow up population Collect M2 seeds from individual plants Plant some seeds from each line Collect tissue and extract DNA Fast Neutron Deletion Mutagenesis-based Reverse Genetics Approach for Plants
  • 31. TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identify point mutations in regions of interest. (McCallum et.al, 2000) (Targeting Induced Local Lesions IN Genomes) TILLING TILLING first began in the late 1990’s by McCallum who worked on characterizing the function of two chromomethylase gene in Arabidopsis.
  • 32.  Development of mutagenized population EMS mutagenesis Development of M2 population  DNA preparation and pooling of individuals  Mutation Discovery PCR amplification of a region of interest Mismatched cleavage Detection of Heteroduplexes as extra peak or band (HPLC or Acrylamide gel) Identification of the mutant individual Sequencing of Mutant PCR product The TILLING Methodology
  • 33. The TILLINGpopulation-MUTAGENESIS Mutagenizing seed with EMS done by soaking seeds in an EMS solution (14-18 h in a 30-100 mM (0.3%-1%) EMS solution.) Planting the seeds in field Mutagenized population (M1generation) is grown to maturity allowed to self-fertilize to produce M2 seeds. M2 seeds can be maintained as lines or bulked If the M2 seed is bulked then lines need to be established using M3 seed. In either case, when sampling M2 plants to establish population
  • 34. Arraying the population for TILLING Genomic DNA is isolated from individuals M2/M3 plants Standardized the DNA concentration of each sample Arrayed in a 96-well microtiter plate Allowing up to 8-fold pooling of diploid plants to increase TILLING throughput
  • 36. Advantages Its applicability to virtually any organism. Its facility for high-throughput and its independence of genome size, reproductive system or generation time. Since it uses Chemical mutagenesis virtually all genes can be targeted by screening few individuals. High degree of mutational saturation can be achieve without excessive collateral DNA damage. Eco- TILLING is useful for association mapping study and linkage disequilibrium analysis. Ecotilling can be used not only to determine the extent of variation but also to assay the level of heterozygosity within a gene.
  • 37. EcoTILLING The first publication of the EcoTILLING method in which TILLING was modified to mine for natural polymorphisms was in 2004 from work in Arabidopsis thaliana. EcoTILLING is similar to TILLING, except that its objective is to identify natural genetic variation as opposed to induced mutations. Many species are not amenable to chemical mutagenesis; therefore, EcoTILLING can aid in the discovery of natural variants and their putative gene function This approach allows one to rapidly screen through many samples with a gene of interest to identify naturally occurring SNPs and / or small INs/DELS.
  • 40. CASE STUDY Forward genetics in a reverse way
  • 41. REFERENCES Azpiroz-Leehan, R., and Feldmann, K.A. (1997).T-DNA insertion mutagenesis in Arabidopsis: Going back and forth. Trends Genet. 13, 152–159. Bradelly J Till et al.,(.2004) Discovery of induced mutation in maize by TILLING:BMC Plant biology.4,471-2229 Krysan, P.J., Young, J.C., and Sussman, M.R. (1999). T-DNA as an insertional mutagen in Arabidopsis. Plant Cell 11, 2283–2290 Parinov, S., and Sundaresan, V. (2000). Functional genomics in Arabidopsis: Large-scale insertional mutagenesis complements the genome sequencing project. Curr. Opin. Biotechnol. 11, 157–161. Sussman, M.R., Amasino, R.M., Young, J.C., Krysan, P.J., and Austin- Phillips, S. (2000). The Arabidopsis knockout facility at the University of Wisconsin-Madison. Plant Physiol. 124, 1465–1467.